Heterocyst-forming Cyanobacterial species encompass the orders Nostocales and Stigonematales. These orders are currently differentiated based solely upon morphological characteristics (such as the formation of true or false branches), which may be unrelated to phylogeny. Thus, these bacteria do not form distinct monophyletic groups in the 16S rRNA tree, and as yet, no reliable molecular markers have yet been identified that allow species of these two orders to be distinguished from each other or from other organisms. Using published genome sequences for these species, we have investigated the relationship of species from these two orders. We describe here detailed phylogenetic analyses based on concatenated protein sequences for 45 proteins from 48 Cyanobacterial species/strains whose genomes are now available. In addition, we have performed comprehensive comparative genomic analyses on eight available Nostocales and Stigonematales genomes to identify conserved signature indels (CSIs) and conserved signature proteins (CSPs) that are specifically present in all Nostocales/Stigonematales or any of their subclades. These analyses have yielded >100 CSIs and CSPs that are specific for distinct coherent clades of Nostocales/Stigonematales. Seventeen of these CSIs and twelve CSPs are present in all sequenced Nostocales and Stigonematales, supporting a distinct relationship of the species from these two orders of heterocyst-forming bacteria. Fifty-four CSIs and forty-one CSPs are specific for different subclades of Nostocales and many others are diagnostic of individual species/strains. The newly-identified CSIs and CSPs, which are specific for different subclades of Nostocales/Stigonematales, may provide novel means for identifying previously unknown members of these orders, for assignment of unsequenced members of heterocystous Cyanobacteria into different identified subclades, and for detecting individual strains from environmental samples by employing CSIs/CSPs as diagnostic tools.Master of Science (MSc
